##
## Attaching package: 'lubridate'
## The following objects are masked from 'package:base':
##
## date, intersect, setdiff, union
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
## Warning: Specifying width/height in layout() is now deprecated.
## Please specify in ggplotly() or plot_ly()
Correlation of growth and duration: -0.2853115
# install.packages("caret")
library(caret)
## Loading required package: lattice
preproc = preProcess(converged)
norm = predict(preproc, converged)
dist = dist(norm, method="euclidian")
## Warning in dist(norm, method = "euclidian"): NAs introduced by coercion
hc = hclust(dist, method="ward.D")
# plot(hc)
clusters = cutree(hc, k=4)
table(clusters)
## clusters
## 1 2 3 4
## 39 15 14 1
c1 = subset(converged, clusters==1)
c1$country
## [1] Andorra Antigua and Barbuda Austria
## [4] Barbados Botswana Bulgaria
## [7] Croatia Cuba Cyprus
## [10] Czechia Denmark Diamond Princess
## [13] Djibouti Eritrea Estonia
## [16] Eswatini Greece Hungary
## [19] Iceland Ireland Israel
## [22] Kosovo Laos Latvia
## [25] Lebanon Lithuania Luxembourg
## [28] Montenegro Netherlands New Zealand
## [31] Niger Norway Poland
## [34] Portugal San Marino Serbia
## [37] Switzerland Tunisia Uruguay
## 187 Levels: Afghanistan Albania Algeria Andorra Angola ... Zimbabwe
# c1: Small countries successfull fighting quickly
c2 = subset(converged, clusters==2)
c2$country
## [1] Angola Brunei
## [3] Chile Ecuador
## [5] Fiji Holy See
## [7] Liechtenstein Nepal
## [9] Papua New Guinea Saint Kitts and Nevis
## [11] Saint Vincent and the Grenadines Slovenia
## [13] Suriname Timor-Leste
## [15] Venezuela
## 187 Levels: Afghanistan Albania Algeria Andorra Angola ... Zimbabwe
# c2: Very small countries successfull fighting quickly
c3 = subset(converged, clusters==3)
c3$country
## [1] Australia Belgium Canada Finland Germany
## [6] Iran Italy Korea, South Russia Spain
## [11] Sri Lanka Taiwan* Thailand Turkey
## 187 Levels: Afghanistan Albania Algeria Andorra Angola ... Zimbabwe
# c3: Misc.
c4 = subset(converged, clusters==4)
c4$country
## [1] US
## 187 Levels: Afghanistan Albania Algeria Andorra Angola ... Zimbabwe
# c4: Large countries
From https://www.cidrap.umn.edu/sites/default/files/public/downloads/cidrap-covid19-viewpoint-part1.pdf average incubation period for COVID-19 is 5 days (range, 2 to 14 days) (Lauer 2020). The longer incubation period for COVID-19 allowed the virus to move silently in different populations before being detected (Kahn 2020, Li 2020). This contributed to an initial environment of complacency before national governments became aware of the severity of the situation The second important factor is the asymptomatic fraction for the two infections. Although information is still being collected to definitively define the asymptomatic fraction for COVID-19, public health officials have stated that 25% of all cases may be asymptomatic (Rettner 2020) and better serologic studies may revise this percentage upward. A number of studies have explored the asymptomatic fraction for influenza; one review found a pooled mean for the asymptomatic fraction of 16% (range of 4% to 28%) (Leung 2015). Thus, while both viruses can lead to asymptomatic infections, the asymptomatic fraction appears to be somewhat higher for COVID-19 than for influenza
Another consideration is the timeframe of presymptomatic viral shedding for people who fall ill. One recent study found that the SARS-CoV-2 viral load was highest at the time of symptom onset, suggesting that viral shedding may peak before symptoms occur, leading to substantial presymptomatic transmission (He 2020). A point-prevalence study of SARS-CoV-2 in nursing home residents showed that, for 27 residents who were asymptomatic at the time of testing, 24 developed symptoms a median of 4 days later (interquartile range, 3 to 5 days) (Arons 2020), supporting the potential for several days of presymptomatic shedding. For the H1N1 pandemic influenza